The Pitt Water Estuary is a shallow, barrier estuary, with typically normal marine salinity, which has been subject to considerable anthropogenic modification. Modern seafloor environments were described using the distribution of sedimentary facies and foraminiferal and ostracod assemblages, examined from surficial sediment samples. Ten sedimentary facies were identified by grouping sediment samples using particle-size distribution data and lithic sand content. Faunal assemblages were identified by cluster analysis, with twelve sample, and eight species associations defined by foraminifera, and eight sample, and six species associations defined by Ostracoda. The distribution of sedimentary facies varies, firstly, with the upstream change in relative current energy (tidal versus fluvial) as reflected by the relative proportion of quartzose to lithic sand in sediment; and, secondly, with the water depth variation in current strength, as reflected by the sand grain size and mud content. The distribution and composition of foraminiferal and ostracod assemblages is determined mainly by average salinity and pH. The position of species along the axis of the estuary correlates with the altered salinity profile inferred to occur during floods, with tolerance to lowered salinity being greater further upstream. Low pH conditions are widely distributed (due to the anoxia of stagnant, nutrient-enriched waters), causing calcareous test dissolution which, in some areas, totally excludes calcareous foraminifera and ostracods. Illumination is also important in controlling ostracod distribution, being lowest in widespread turbid waters. Additional factors controlling foraminiferal and ostracod distribution include: substrate mobility, nutrients, seagrass distribution, tidal exposure, and tolerance to varying temperature. Recent seafloor environments were described using the distribution of sediments, foraminifera and ostracods in short cores and previous spatial surveys. They have changed considerably since the late 19th century, mainly as a result of human activities which continue to affect the estuary. During periods of increased agricultural activity (1920's-1940s; 1960's-present), greater land clearance, cultivation and fertiliser usage within the catchment area lead to increased sediment and nutrient loading of fluvial waters entering the estuary. This lead to increased sedimentation, mud accumulation, turbidity, and lowered dissolved oxygen and pH within the estuary, causing the demise of dense clam and oyster beds, reduced distribution of ostracods and calcareous foraminifera, increased distribution of agglutinated foraminifera, and increased faunal abundance within nutrient-enriched sediments. Dam construction and irrigation activities during the 20th century, reduced rainfall over the last thirty years, and causeway construction during the 1870's, have all contributed to increased water stagnation, reduced flushing, and more upstream penetration of the estuary by marine waters.